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Protein Structure Prediction pp 337–353Cite as

Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASS

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2165))

Abstract

Conformational flexibility of protein structures can play an important role in protein function. The flexibility is often studied using computational methods since experimental characterization can be difficult. Depending on protein system size, computational tools may require large computational resources or significant simplifications in the modeled systems to speed up calculations. In this work, we present the protocols for efficient simulations of flexibility of folded protein structures that use coarse-grained simulation tools of different resolutions: medium, represented by CABS-flex, and low, represented by SUPRASS. We test the protocols using a set of 140 globular proteins and compare the results with structure fluctuations observed in MD simulations, ENM modeling, and NMR ensembles. As demonstrated, CABS-flex predictions show high correlation to experimental and MD simulation data, while SURPASS is less accurate but promising in terms of future developments.

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Acknowledgments

A.E.B-D, A.K., and S.K. received funding from NCN Poland, Grant MAESTRO2014/14/A/ST6/00088.

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Authors and Affiliations

  1. Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland

    Aleksandra E. Badaczewska-Dawid, Andrzej Kolinski & Sebastian Kmiecik

  2. Department of Chemistry, Iowa State University, Ames, IA, USA

    Aleksandra E. Badaczewska-Dawid

Authors
  1. Aleksandra E. Badaczewska-Dawid
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  2. Andrzej Kolinski
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  3. Sebastian Kmiecik
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Corresponding author

Correspondence to Sebastian Kmiecik .

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Editors and Affiliations

  1. Department of Computer Science, Purdue University, West Lafayette, IN, USA

    Daisuke Kihara

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Badaczewska-Dawid, A.E., Kolinski, A., Kmiecik, S. (2020). Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASS. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 2165. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0708-4_20

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  • DOI: https://doi.org/10.1007/978-1-0716-0708-4_20

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0707-7

  • Online ISBN: 978-1-0716-0708-4

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